Rust. RUST. RUST.
Depending on what your after if you want something with a little "get up and go" the 4.0 inline six is the only way to go. Other wise the 2.5 4cyl is the next best thing, utterly bomb proof, its just about as powerful as a pencil sharpener.

The place to really check for rust is the frame underneath and the floor pans.
Everywhere else it rusts is readily visible. Around the flares, below the doors, etc.

4X4 doesn't mean it has a 4.0. It could be a 2.5. If it is a manual transmission, check for hydraulic leakage. The slave cylinder will leak inside the bellhousing.
The master cylinder will leak behind the fuse panel under the dash. If it has not been maintained, it will most likely leak oil from a number of places. Valve cover, rear main, oil pan, etc. All easily fixed but many times ignored by owners.

Other than that, just check as cracker said. No weird noises from the driveline. check for frame alignment.

Get as much history as you can.

These are really reliable trucks and can be maintained forever if you want. The motors and driveline parts are readily available.

From the doors forward, everything from a Cherokee will interchange. From behind the doors, the Comanche stuff is unique.

Go over to comancheclub.com. Everything you ever wanted to know about these trucks is over there.